Repository Index

Code for running RFdiffusion

ProtTrans is providing state of the art pretrained language models for proteins. ProtTrans was trained on thousands of GPUs from Summit and hundreds of Google TPUs using Transformers Models.

Scientific workflow engine designed for simplicity & scalability. Trivially transition between one off use cases to massive scale production environments

• workflow-execution
• workflow
• cloud
• hpc

ADAM is a genomics analysis platform with specialized file formats built using Apache Avro, Apache Spark, and Apache Parquet. Apache 2 licensed.

• spark
• big-data
• bioinformatics
• genomics

Generation of protein sequences and evolutionary alignments via discrete diffusion models

• discrete-diffusion
• generative-model
• multiple-sequence-alignment
• protein-sequences

Lightweight, super fast C/C++ (& Python) library for sequence alignment using edit (Levenshtein) distance.

• sequence-alignment
• edit-distance
• levehnstein-distance
• library

A Practical and Efficient NCBI Taxonomy Toolkit, also supports creating NCBI-style taxdump files for custom taxonomies like GTDB/ICTV

• bioinformatics
• taxonomy
• cross-platform
• lineage

Native R and Python sample-deletion robustness for omics: candidate certificates, minimum deletion bounds, Bioconductor model refits and donor-level pseudobulk

• bioinformatics
• exact-optimization
• metabolomics
• paired-data

Bi-Directional Equivariant Long-Range DNA Sequence Modeling

talk with NCBI entrez using R

• r
• rstats
• r-package

A Python package for the identification, characterization and comparison of spatial clusters from spatial -omics data.

Probabilistic cell segmentation for in situ spatial transcriptomics

OpenBioLink is a resource and evaluation framework for evaluating link prediction models on heterogeneous biomedical graph data.

NeoDTI: Neural integration of neighbor information from a heterogeneous network for discovering new drug-target interactions

• computational-biology
• bioinformatics
• graph-convolution
• deep-learning

3D shape analysis using deep learning

• cancer-biology
• cell-biology
• deep-learning
• geometric-deep-learning

Data logistics system enabling real-time pathogen surveillance. Built for the Seattle Flu Study.

• postgres
• postgresql
• python
• infectious-disease